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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2016-07-12 23:42:39 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2016-07-12 23:42:39 +0200
commit57ee10981824b082fe40f0bfa24ac8e9b6ddf98b (patch)
treea16a27217a77b16cf1a1f16dba2f9054ecab1b2f
parentdev-java/htsjdk: make gradle use relocated $HOME/.gradle/ inside sanbox paths (diff)
parentdev-python/pyfftw: Add scipy to deps (diff)
downloadsci-57ee10981824b082fe40f0bfa24ac8e9b6ddf98b.tar.gz
sci-57ee10981824b082fe40f0bfa24ac8e9b6ddf98b.tar.bz2
sci-57ee10981824b082fe40f0bfa24ac8e9b6ddf98b.zip
Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci
-rw-r--r--dev-python/pyfftw/Manifest2
-rw-r--r--dev-python/pyfftw/pyfftw-0.10.4.ebuild (renamed from dev-python/pyfftw/pyfftw-0.10.1.ebuild)1
-rw-r--r--dev-python/pyfftw/pyfftw-9999.ebuild1
-rw-r--r--sci-biology/ants/ants-9999.ebuild4
-rw-r--r--sci-libs/dealii/Manifest2
-rw-r--r--sci-libs/dealii/dealii-8.1.0-r2.ebuild121
-rw-r--r--sci-libs/dealii/dealii-8.4.1-r1.ebuild (renamed from sci-libs/dealii/dealii-8.4.1.ebuild)1
-rw-r--r--sci-libs/dealii/dealii-9999.ebuild9
-rw-r--r--sci-libs/dealii/files/dealii-8.1.0-p4est1.0-support.patch271
-rw-r--r--sci-libs/trilinos/Manifest4
-rw-r--r--sci-libs/trilinos/trilinos-11.10.2.ebuild202
-rw-r--r--sci-libs/trilinos/trilinos-11.12.1-r1.ebuild202
-rw-r--r--sci-libs/trilinos/trilinos-11.14.1-r1.ebuild3
-rw-r--r--sci-libs/trilinos/trilinos-12.0.1.ebuild3
-rw-r--r--sci-libs/trilinos/trilinos-12.2.1.ebuild3
-rw-r--r--sci-libs/trilinos/trilinos-12.6.3.ebuild (renamed from sci-libs/trilinos/trilinos-12.6.2.ebuild)3
-rw-r--r--sci-mathematics/petsc/Manifest5
-rw-r--r--sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch18
-rw-r--r--sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch17
-rw-r--r--sci-mathematics/petsc/petsc-3.5.4.ebuild (renamed from sci-mathematics/petsc/petsc-3.5.3.ebuild)4
-rw-r--r--sci-mathematics/petsc/petsc-3.6.3.ebuild247
-rw-r--r--sci-mathematics/petsc/petsc-3.7.2.ebuild (renamed from sci-mathematics/petsc/petsc-3.6.0.ebuild)18
22 files changed, 72 insertions, 1069 deletions
diff --git a/dev-python/pyfftw/Manifest b/dev-python/pyfftw/Manifest
index 2087df709..e68e225fc 100644
--- a/dev-python/pyfftw/Manifest
+++ b/dev-python/pyfftw/Manifest
@@ -1,2 +1,2 @@
-DIST pyFFTW-0.10.1.tar.gz 350018 SHA256 fe1c45154ecebbe1f765db25fdb774d09b17178f520b6be74ef6e213b899099d SHA512 8e1a8e8d30d65a0d9b97986c32483ae917ec66c034db6b027ec4a30ff924a08e23b6b55e6479130655fa9964ce6b3f0f7413bd800e641c88ff4b1b11b7a6bfe3 WHIRLPOOL dc0bd4c185398e1c3a3d0427b948d0cf8b79bc73b3203e48b68bcee1ee478ecb552bd36848b96bcdee13ce7e98efc3ae6cd0f36007c792c8e8dfd1a1f86cfcd5
+DIST pyFFTW-0.10.4.tar.gz 365496 SHA256 739b436b7c0aeddf99a48749380260364d2dc027cf1d5f63dafb5f50068ede1a SHA512 6848133e30a02ee51bb86613f53a5fdbf9b5a0fea3cab01b8ca7d365f924a966ac9b94f4ed62979d418f9f847369f8c50568ca855e472035fa37e86e630fb9fd WHIRLPOOL faa0859adbe1ee7235ddc799581e5741e066c3884ce29a4dadecf1f448d3fc03cac4c7e2bd60e09af25aef22442b52f0fcf10343ac93a0575c72ecbe66a6ff11
DIST pyFFTW-0.9.2.tar.gz 336928 SHA256 f6bbb6afa93085409ab24885a1a3cdb8909f095a142f4d49e346f2bd1b789074 SHA512 f77e52ce36c9375dbd48ebfd848884c9d9a1e080df920f28f10db5350549011de62fa1cb3ec96d1b1450d8a45209e97a0b20ece43eea16d7e543581c8444d194 WHIRLPOOL 473759c40cb6701edde861e7ecb681c5091a4aa3a678e448bd840c944a2f4f6965a9b843989b076cdbf05dbb1ea3204f1555033fb985a8210ae4ad3c872f8241
diff --git a/dev-python/pyfftw/pyfftw-0.10.1.ebuild b/dev-python/pyfftw/pyfftw-0.10.4.ebuild
index 60229367a..5dc71b46d 100644
--- a/dev-python/pyfftw/pyfftw-0.10.1.ebuild
+++ b/dev-python/pyfftw/pyfftw-0.10.4.ebuild
@@ -22,6 +22,7 @@ S="${WORKDIR}/${MY_PN}-${PV}"
RDEPEND="
>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
>=sci-libs/fftw-3.3.3
>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
"
diff --git a/dev-python/pyfftw/pyfftw-9999.ebuild b/dev-python/pyfftw/pyfftw-9999.ebuild
index 812f0afc0..e1312f34b 100644
--- a/dev-python/pyfftw/pyfftw-9999.ebuild
+++ b/dev-python/pyfftw/pyfftw-9999.ebuild
@@ -19,6 +19,7 @@ IUSE="test"
RDEPEND="
>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
>=sci-libs/fftw-3.3.3
>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
"
diff --git a/sci-biology/ants/ants-9999.ebuild b/sci-biology/ants/ants-9999.ebuild
index d3e39dbbe..2565a5a19 100644
--- a/sci-biology/ants/ants-9999.ebuild
+++ b/sci-biology/ants/ants-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -15,7 +15,7 @@ SLOT="0"
LICENSE="BSD"
KEYWORDS=""
-DEPEND="sci-libs/itk"
+DEPEND=""
RDEPEND="${DEPEND}"
src_install() {
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
index 5fbe9683a..cd7c25bce 100644
--- a/sci-libs/dealii/Manifest
+++ b/sci-libs/dealii/Manifest
@@ -1,5 +1,3 @@
-DIST dealii-8.1.0-offline_documentation.tar.gz 96865280 SHA256 c39f309ff5296a05dfdc1b8e585ddcfe658794f16bbd9f235bdf7b5e00558b65 SHA512 9ff9ab5bcdbe3b1d127a6580f9b5d39dfc5b3840ff9278496c71b56bd5e2e33a781a0d555f08e46fdf96847510e58960ad2cf144e9d48aea31fc5080961a1e7b WHIRLPOOL e841c440899fc5a933501bfdf6c8694863678382cd223d0941af0649b6452218e53e912c53be9cee4588e0be657dad8cc521ad162189cbfb5a39fbf9f4fe71cf
-DIST dealii-8.1.0.tar.gz 13353502 SHA256 d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99 SHA512 9d6e913e7a8c54f386839d031f2931a74e8ac6e7db8693c201a11ec6ca34962626a42a57b727297c9f3d8b9efebddb4f2397c27bbee4212e726ce2714f1c3f70 WHIRLPOOL 8cd7aeb47c28bc473bb24d1632f6074de893b20d995d6077c80b88834693b8f9ad1aee181b7abda55a5567efa6c6d169da4c6061cd939b63351330f7e4b767c5
DIST dealii-8.2.1-offline_documentation.tar.gz 98861605 SHA256 4622e8ef96c5105dc9cf6e35c54a6fd072956235320646c4f53b5def7748b2fd SHA512 721d963991d53f2c23010f6c398cddd9e058385375a3a77245fbe95b10dbfe1a452d1c2ead2cb8d8a0174b0b2262ed40832f100a545af49dc923d19f42e8e283 WHIRLPOOL 5a1d070d8336c9d9a3a582a73457fa1831f737ecd5def1787bcbffef30f718eef03c57c58ea80e79d6735b73d6f8c83d498a366f002fa5078ef51c71af74b2f9
DIST dealii-8.2.1.tar.gz 13667634 SHA256 d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0 SHA512 9cd3ed9a4330aa7464ecfe92677fcddae0aadcca7885c898eb8a746caa30fff587ccf5614cec61ffb6b27280c94b423d6370661a1791c601d7abce163502daeb WHIRLPOOL d7b86adcf7dc5dddf63aac4d37be6512aff9889279eb58f9d79cbc5d0c467a1ba50892a08495057f20a3352767f88a42bff7d82f9ba2b5567b02511cb806b7f5
DIST dealii-8.3.0-offline_documentation.tar.gz 152228920 SHA256 474b1b64a392b1a77b3e628b4c5f83099ed3b4cd5bc87966454645607f2f3851 SHA512 f3ba395204b18b9b8a0e5a1ea0d59260f3ed556d866820c78ed52d9fd16cc4702870eec9bfa0a3e6996696256f6d371d88a9642392eab135291f6a2411038c48 WHIRLPOOL aabcb6b951f1331fbf1cc0cef3f9dc92f8f4c08698f6ddbafff9b5a59d4344bab75346d353cb9b4582e8233230598501d13eecfa021a52e5692fcd3849581ba0
diff --git a/sci-libs/dealii/dealii-8.1.0-r2.ebuild b/sci-libs/dealii/dealii-8.1.0-r2.ebuild
deleted file mode 100644
index 4beb1fe18..000000000
--- a/sci-libs/dealii/dealii-8.1.0-r2.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils eutils multilib
-
-# deal.II uses its own FindLAPACK.cmake file that calls into the system
-# FindLAPACK.cmake module and does additional internal setup. Do not remove
-# any of these modules:
-CMAKE_REMOVE_MODULES_LIST=""
-
-DESCRIPTION="Solving partial differential equations with the finite element method"
-HOMEPAGE="http://www.dealii.org/"
-
-if [[ ${PV} = *9999* ]]; then
- inherit git-r3
- EGIT_REPO_URI="git://github.com/dealii/dealii.git"
- SRC_URI=""
- KEYWORDS=""
-else
- SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz
- doc? ( https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}-offline_documentation.tar.gz )"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
- S="${WORKDIR}/deal.II"
-fi
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-IUSE="
- arpack cpu_flags_x86_avx cpu_flags_x86_sse2 +debug doc +examples hdf5
- +lapack mesh_converter metis mpi mumps netcdf p4est parameter_gui petsc
- +sparse static-libs +tbb trilinos
-"
-
-# TODO: add slepc use flag once slepc is packaged for gentoo-science
-REQUIRED_USE="
- mumps? ( mpi lapack )
- p4est? ( mpi )
- trilinos? ( mpi )"
-
-RDEPEND="dev-libs/boost
- app-arch/bzip2
- sys-libs/zlib
- arpack? ( sci-libs/arpack[mpi=] )
- hdf5? ( sci-libs/hdf5[mpi=] )
- lapack? ( virtual/lapack )
- metis? ( >=sci-libs/parmetis-4 )
- mpi? ( virtual/mpi )
- mumps? ( sci-libs/mumps[mpi] )
- netcdf? ( sci-libs/netcdf-cxx:0 )
- p4est? ( sci-libs/p4est[mpi] )
- parameter_gui? ( dev-qt/qtgui:4 )
- petsc? ( sci-mathematics/petsc[mpi=] )
- sparse? ( sci-libs/umfpack )
- tbb? ( dev-cpp/tbb )
- trilinos? ( sci-libs/trilinos )"
-
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- doc? ( app-doc/doxygen[dot] dev-lang/perl )"
-
-src_configure() {
- # deal.II needs a custom build type:
- local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
-
- local mycmakeargs=(
- -DDEAL_II_ALLOW_AUTODETECTION=OFF
- -DDEAL_II_ALLOW_BUNDLED=OFF
- -DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
- -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
- -DDEAL_II_COMPONENT_COMPAT_FILES=OFF
- -DDEAL_II_CMAKE_MACROS_RELDIR=share/${PN}/cmake/macros
- -DDEAL_II_DOCHTML_RELDIR=share/doc/${PF}/html
- -DDEAL_II_DOCREADME_RELDIR=share/doc/${PF}/
- -DDEAL_II_EXAMPLES_RELDIR=share/doc/${PF}/examples
- -DDEAL_II_LIBRARY_RELDIR=$(get_libdir)
- -DDEAL_II_WITH_BZIP2=ON
- -DDEAL_II_WITH_ZLIB=ON
- $(cmake-utils_use arpack DEAL_II_WITH_ARPACK)
- $(cmake-utils_use cpu_flags_x86_avx DEAL_II_HAVE_AVX)
- $(cmake-utils_use cpu_flags_x86_sse2 DEAL_II_HAVE_SSE2)
- $(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION)
- $(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES)
- $(cmake-utils_use hdf5 DEAL_II_WITH_HDF5)
- $(cmake-utils_use lapack DEAL_II_WITH_LAPACK)
- $(cmake-utils_use mesh_converter DEAL_II_COMPONENT_MESH_CONVERTER)
- $(cmake-utils_use metis DEAL_II_WITH_METIS)
- $(cmake-utils_use mpi DEAL_II_WITH_MPI)
- $(cmake-utils_use mumps DEAL_II_WITH_MUMPS)
- $(cmake-utils_use netcdf DEAL_II_WITH_NETCDF)
- $(cmake-utils_use p4est DEAL_II_WITH_P4EST)
- $(cmake-utils_use parameter_gui DEAL_II_COMPONENT_PARAMETER_GUI)
- $(cmake-utils_use petsc DEAL_II_WITH_PETSC)
- $(cmake-utils_use sparse DEAL_II_WITH_UMFPACK)
- $(cmake-utils_use !static-libs BUILD_SHARED_LIBS)
- $(cmake-utils_use static-libs DEAL_II_PREFER_STATIC_LIBS)
- $(cmake-utils_use tbb DEAL_II_WITH_THREADS)
- $(cmake-utils_use trilinos DEAL_II_WITH_TRILINOS)
- )
- cmake-utils_src_configure
-}
-
-src_install() {
- DOCS=( README )
-
- if use doc && [[ ${PV} != *9999* ]]; then
- # copy missing images to the build directory:
- cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
- "${BUILD_DIR}"/doc/doxygen/deal.II || die
- # replace links:
- sed -i \
- 's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
- "${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
- fi
- cmake-utils_src_install
-
- # decompress the installed example sources:
- use examples && docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-libs/dealii/dealii-8.4.1.ebuild b/sci-libs/dealii/dealii-8.4.1-r1.ebuild
index 4db725686..d572f07db 100644
--- a/sci-libs/dealii/dealii-8.4.1.ebuild
+++ b/sci-libs/dealii/dealii-8.4.1-r1.ebuild
@@ -79,6 +79,7 @@ src_configure() {
-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
-DDEAL_II_SHARE_RELDIR="share/${PN}"
-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
+ -DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
-DDEAL_II_WITH_BZIP2=ON
-DDEAL_II_WITH_ZLIB=ON
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
index 4db725686..4aa4fbf7b 100644
--- a/sci-libs/dealii/dealii-9999.ebuild
+++ b/sci-libs/dealii/dealii-9999.ebuild
@@ -35,8 +35,8 @@ LICENSE="LGPL-2.1+"
SLOT="0"
IUSE="
arpack cpu_flags_x86_avx cpu_flags_x86_sse2 c++11 +debug doc +examples
- hdf5 +lapack metis mpi muparser opencascade netcdf p4est parameter_gui
- petsc +sparse static-libs +tbb trilinos
+ +gsl hdf5 +lapack metis mpi muparser opencascade netcdf p4est petsc
+ +sparse static-libs +tbb trilinos
"
# TODO: add slepc use flag once slepc is packaged for gentoo-science
@@ -48,6 +48,7 @@ RDEPEND="dev-libs/boost
app-arch/bzip2
sys-libs/zlib
arpack? ( sci-libs/arpack[mpi=] )
+ gsl? ( sci-libs/gsl )
hdf5? ( sci-libs/hdf5[mpi=] )
lapack? ( virtual/lapack )
metis? ( >=sci-libs/parmetis-4 )
@@ -56,7 +57,6 @@ RDEPEND="dev-libs/boost
netcdf? ( sci-libs/netcdf-cxx:0 )
opencascade? ( sci-libs/opencascade:* )
p4est? ( sci-libs/p4est[mpi] )
- parameter_gui? ( dev-qt/qtgui:4 )
petsc? ( sci-mathematics/petsc[mpi=] )
sparse? ( sci-libs/umfpack )
tbb? ( dev-cpp/tbb )
@@ -79,6 +79,7 @@ src_configure() {
-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
-DDEAL_II_SHARE_RELDIR="share/${PN}"
-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
+ -DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
-DDEAL_II_WITH_BZIP2=ON
-DDEAL_II_WITH_ZLIB=ON
@@ -88,6 +89,7 @@ src_configure() {
$(cmake-utils_use cpu_flags_x86_sse2 DEAL_II_HAVE_SSE2)
$(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION)
$(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES)
+ $(cmake-utils_use gsl DEAL_II_WITH_GSL)
$(cmake-utils_use hdf5 DEAL_II_WITH_HDF5)
$(cmake-utils_use lapack DEAL_II_WITH_LAPACK)
$(cmake-utils_use metis DEAL_II_WITH_METIS)
@@ -97,7 +99,6 @@ src_configure() {
-DOPENCASCADE_DIR="${CASROOT}"
$(cmake-utils_use opencascade DEAL_II_WITH_OPENCASCADE)
$(cmake-utils_use p4est DEAL_II_WITH_P4EST)
- $(cmake-utils_use parameter_gui DEAL_II_COMPONENT_PARAMETER_GUI)
$(cmake-utils_use petsc DEAL_II_WITH_PETSC)
$(cmake-utils_use sparse DEAL_II_WITH_UMFPACK)
$(cmake-utils_use !static-libs BUILD_SHARED_LIBS)
diff --git a/sci-libs/dealii/files/dealii-8.1.0-p4est1.0-support.patch b/sci-libs/dealii/files/dealii-8.1.0-p4est1.0-support.patch
deleted file mode 100644
index 3ef8d99e0..000000000
--- a/sci-libs/dealii/files/dealii-8.1.0-p4est1.0-support.patch
+++ /dev/null
@@ -1,271 +0,0 @@
-Upstream commits:
- 4b6a6a9aae750941723890c44f0cb3326e5ba87b
- 67d70862aa2b2c2e925a2b1262c9934ea0f9a873
- dc0308a408360bfa5e21a58d10c2c2a7dca3a8ad
-
-diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc
-index 5687fae..a6e5e85 100644
---- a/source/distributed/tria.cc
-+++ b/source/distributed/tria.cc
-@@ -155,10 +155,17 @@ namespace internal
- types<2>::balance_type btype,
- p4est_init_t init_fn);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ p4est_gloidx_t (&partition) (types<2>::forest *p4est,
-+ int partition_for_coarsening,
-+ p4est_weight_t weight_fn);
-+#else
- static
- void (&partition) (types<2>::forest *p4est,
- int partition_for_coarsening,
- p4est_weight_t weight_fn);
-+#endif
-
- static
- void (&save) (const char *filename,
-@@ -173,16 +180,28 @@ namespace internal
- void *user_pointer,
- types<2>::connectivity **p4est);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ int (&connectivity_save) (const char *filename,
-+ types<2>::connectivity *connectivity);
-+#else
- static
- void (&connectivity_save) (const char *filename,
- types<2>::connectivity *connectivity);
-+#endif
-
- static
- int (&connectivity_is_valid) (types<2>::connectivity *connectivity);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ types<2>::connectivity *(&connectivity_load) (const char *filename,
-+ long unsigned *length);
-+#else
- static
- types<2>::connectivity *(&connectivity_load) (const char *filename,
- long *length);
-+#endif
-
- static
- unsigned int (&checksum) (types<2>::forest *p4est);
-@@ -301,10 +320,17 @@ namespace internal
- p4est_init_t init_fn)
- = p4est_balance;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ p4est_gloidx_t (&functions<2>::partition) (types<2>::forest *p4est,
-+ int partition_for_coarsening,
-+ p4est_weight_t weight_fn)
-+ = p4est_partition_ext;
-+#else
- void (&functions<2>::partition) (types<2>::forest *p4est,
- int partition_for_coarsening,
- p4est_weight_t weight_fn)
- = p4est_partition_ext;
-+#endif
-
- void (&functions<2>::save) (const char *filename,
- types<2>::forest *p4est,
-@@ -320,18 +346,31 @@ namespace internal
- types<2>::connectivity **p4est)
- = p4est_load;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ int (&functions<2>::connectivity_save) (const char *filename,
-+ types<2>::connectivity *connectivity)
-+ = p4est_connectivity_save;
-+#else
- void (&functions<2>::connectivity_save) (const char *filename,
- types<2>::connectivity *connectivity)
- = p4est_connectivity_save;
-+#endif
-
- int (&functions<2>::connectivity_is_valid) (types<2>::connectivity
- *connectivity)
- = p4est_connectivity_is_valid;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ types<2>::connectivity *
-+ (&functions<2>::connectivity_load) (const char *filename,
-+ long unsigned *length)
-+ = p4est_connectivity_load;
-+#else
- types<2>::connectivity *
- (&functions<2>::connectivity_load) (const char *filename,
- long *length)
- = p4est_connectivity_load;
-+#endif
-
- unsigned int (&functions<2>::checksum) (types<2>::forest *p4est)
- = p4est_checksum;
-@@ -451,10 +490,17 @@ namespace internal
- types<3>::balance_type btype,
- p8est_init_t init_fn);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ p4est_gloidx_t (&partition) (types<3>::forest *p8est,
-+ int partition_for_coarsening,
-+ p8est_weight_t weight_fn);
-+#else
- static
- void (&partition) (types<3>::forest *p8est,
- int partition_for_coarsening,
- p8est_weight_t weight_fn);
-+#endif
-
- static
- void (&save) (const char *filename,
-@@ -469,16 +515,28 @@ namespace internal
- void *user_pointer,
- types<3>::connectivity **p4est);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ int (&connectivity_save) (const char *filename,
-+ types<3>::connectivity *connectivity);
-+#else
- static
- void (&connectivity_save) (const char *filename,
- types<3>::connectivity *connectivity);
-+#endif
-
- static
- int (&connectivity_is_valid) (types<3>::connectivity *connectivity);
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ static
-+ types<3>::connectivity *(&connectivity_load) (const char *filename,
-+ long unsigned *length);
-+#else
- static
- types<3>::connectivity *(&connectivity_load) (const char *filename,
- long *length);
-+#endif
-
- static
- unsigned int (&checksum) (types<3>::forest *p8est);
-@@ -600,10 +658,17 @@ namespace internal
- p8est_init_t init_fn)
- = p8est_balance;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ p4est_gloidx_t (&functions<3>::partition) (types<3>::forest *p8est,
-+ int partition_for_coarsening,
-+ p8est_weight_t weight_fn)
-+ = p8est_partition_ext;
-+#else
- void (&functions<3>::partition) (types<3>::forest *p8est,
- int partition_for_coarsening,
- p8est_weight_t weight_fn)
- = p8est_partition_ext;
-+#endif
-
- void (&functions<3>::save) (const char *filename,
- types<3>::forest *p4est,
-@@ -619,18 +684,31 @@ namespace internal
- types<3>::connectivity **p4est)
- = p8est_load;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ int (&functions<3>::connectivity_save) (const char *filename,
-+ types<3>::connectivity *connectivity)
-+ = p8est_connectivity_save;
-+#else
- void (&functions<3>::connectivity_save) (const char *filename,
- types<3>::connectivity *connectivity)
- = p8est_connectivity_save;
-+#endif
-
- int (&functions<3>::connectivity_is_valid) (types<3>::connectivity
- *connectivity)
- = p8est_connectivity_is_valid;
-
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ types<3>::connectivity *
-+ (&functions<3>::connectivity_load) (const char *filename,
-+ long unsigned *length)
-+ = p8est_connectivity_load;
-+#else
- types<3>::connectivity *
- (&functions<3>::connectivity_load) (const char *filename,
- long *length)
- = p8est_connectivity_load;
-+#endif
-
- unsigned int (&functions<3>::checksum) (types<3>::forest *p8est)
- = p8est_checksum;
-diff --git a/cmake/modules/FindP4EST.cmake b/cmake/modules/FindP4EST.cmake
-index f2bf417..44846c7 100644
---- a/cmake/modules/FindP4EST.cmake
-+++ b/cmake/modules/FindP4EST.cmake
-@@ -179,17 +179,28 @@
- STRING(REGEX REPLACE
- "^[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1"
- P4EST_VERSION_SUBMINOR "${P4EST_VERSION}")
--
-- # Now for the patch number such as in 0.3.4.1. If there
-- # is no patch number, then the REGEX REPLACE will fail,
-- # setting P4EST_VERSION_PATCH to P4EST_VERSION. If that
-- # is the case, then set the patch number to zero
- STRING(REGEX REPLACE
-- "^[0-9]+\\.[0-9]+\\.[0-9]+\\.([0-9]+)?.*$" "\\1"
-+ "^[0-9]+\\.[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1"
- P4EST_VERSION_PATCH "${P4EST_VERSION}")
-- IF(${P4EST_VERSION_PATCH} STREQUAL "${P4EST_VERSION}")
-+
-+ #
-+ # We cannot rely on the fact that SUBMINOR or PATCH are defined.
-+ # Nevertheless, we need a full version number for our preprocessor macros
-+ # to work. If the p4est version number is only of the form x.y instead of
-+ # a.b.c.d, then the last two REGEX_REPLACE calls above will have failed
-+ # because the regular expression didn't match the version string,
-+ # and P4EST_VERSION_SUBMINOR and P4EST_VERSION_PATCH will either be
-+ # empty or be the full version string. In those cases, set those numbers
-+ # to 0 if necessary.
-+ #
-+ IF("${P4EST_VERSION_SUBMINOR}" MATCHES "^(|${P4EST_VERSION})$")
-+ SET(P4EST_VERSION_SUBMINOR "0")
-+ ENDIF()
-+
-+ IF("${P4EST_VERSION_PATCH}" MATCHES "^(|${P4EST_VERSION})$")
- SET(P4EST_VERSION_PATCH "0")
- ENDIF()
-+
-
-
- MARK_AS_ADVANCED(P4EST_DIR)
-diff --git a/include/deal.II/distributed/tria.h b/include/deal.II/distributed/tria.h
-index ea3e88b..8daa70d 100644
---- a/include/deal.II/distributed/tria.h
-+++ b/include/deal.II/distributed/tria.h
-@@ -88,7 +88,11 @@ namespace internal
- typedef p4est_quadrant_t quadrant;
- typedef p4est_topidx_t topidx;
- typedef p4est_locidx_t locidx;
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ typedef p4est_connect_type_t balance_type;
-+#else
- typedef p4est_balance_type_t balance_type;
-+#endif
- typedef p4est_ghost_t ghost;
- };
-
-@@ -101,7 +105,11 @@ namespace internal
- typedef p8est_quadrant_t quadrant;
- typedef p4est_topidx_t topidx;
- typedef p4est_locidx_t locidx;
-+#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
-+ typedef p8est_connect_type_t balance_type;
-+#else
- typedef p8est_balance_type_t balance_type;
-+#endif
- typedef p8est_ghost_t ghost;
- };
-
diff --git a/sci-libs/trilinos/Manifest b/sci-libs/trilinos/Manifest
index 5a5afc9d8..3c7a0c3df 100644
--- a/sci-libs/trilinos/Manifest
+++ b/sci-libs/trilinos/Manifest
@@ -1,6 +1,4 @@
-DIST trilinos-11.10.2-Source.tar.gz 127593733 SHA256 03c435d40157857fecca5db79c1e307ab683857ff2aa60f1c15926c8c4a4e0e2 SHA512 2accdc5500b486312741f44ce7b3e166cd6a38a98e9accb4d59e20f2dd145f78904f1149fc40eb9b00d63fcafd99dcd8bca0f55e06d809a7224f387afc0dabcc WHIRLPOOL 9fc5a0419aa8d43b0bd9bd0d5049a0b441a1921bc317322986f081952c1308f3f96b36a5fdb0eecb5de0ab3faeb6773885a61c631e6ffd59e02e728cfc7c9648
-DIST trilinos-11.12.1-Source.tar.gz 138102285 SHA256 a86861a630a4d516d9f7e7512402b4696a3a8eec9c4b0c639af72b4cc2bcece9 SHA512 da538c42e56e82c530d10ff5e5c7edee8c1f54ccd9730bfd9b63c284d28ace932cc4aa591817c314d1a0df9bb469efbe03244feacf1f452d90b98419d041d000 WHIRLPOOL 2482a108123609f8f9e4c8fbade68d91814861b35202ede2f07c40b62802c6337a4dc1da80d95489744b5bfbf8098726bd36ee29d804afc358b9a33ba306a7b6
DIST trilinos-11.14.1-Source.tar.gz 132562115 SHA256 bc538eb8cef4e38ac45efdd5ce4601908339483581d138f91d2354299c547867 SHA512 136ba9304897be1c5b13f31f5bb1c27dc64b5d8473316d6ca13bc79c6a116262420ac005d35ca984afb4776072916fafff826f8057aed80ea243e528b86e127f WHIRLPOOL a4c9447ee490450623b045d8c89280f6427a7692b5450462d87cb7b493791044efb1e460f6784b7a674aaf7a02c67b1a728fa0d837acdc04e26a9594a7b82ea6
DIST trilinos-12.0.1-Source.tar.gz 133951053 SHA256 ca252d9a544de16b7e1555985428d8ed8518959fd2cdbcba31688bd1a84f6605 SHA512 a317765d254bef0252fa90df91b02d9dbfd26bc8507019fce65b4e9b897cde221daaab34f87c0e20b4439d978090020847bd007b23b5bdc1258c3e4db633708a WHIRLPOOL f60a6cd7fa0f9fed385e1d4f691e6f7304658a931c5e77117991c05af5df1cebad613de007ddc13a53711c05cc3180c1a4623ac4c41aed22b1fe16780ff7771f
DIST trilinos-12.2.1-Source.tar.gz 132615497 SHA256 3aa998ade0f81f34fc630ec5da5d52148382648deb9ad54f4cdcdf4eefb34e66 SHA512 782080f8719688242d0e28f4a5cc592700d61122fc209bf1739f941f82f70275455af84b85b1ee297b435bf2df0680c0542ee73aa7b60a990b56429ff9a87311 WHIRLPOOL c98c258b9490041eed6e8f93b119bcb3aa534819b37f0e766b3b9d2c7d4683b1098d9f496dcd114a6b9c4ca293881af9c1a23ce175709103f87de24f5f310d9b
-DIST trilinos-12.6.2-Source.tar.gz 99521342 SHA256 0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9 SHA512 04cc14411f3e90b6c9dc285e89b937e033b33edfae0ddbc9492caa6f57af7b9c5e43c74aaca01c9b69b3dcfd7adcdb80d4e6b8b97f837cb612a8040ee2a071fa WHIRLPOOL e46527cd4e3a09d8e7bef720bcd5cf422b68a66ad328aa1b4aaa1f1aad60c6124d6117d1b1b778c9493857104f532c7eeb6ddaccb4f8fa15ebe9c1dea260d98c
+DIST trilinos-12.6.3-Source.tar.gz 99519655 SHA256 960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e SHA512 ce534cf4733c348e6b9bab493014f746eb6e24bf90e0cf30dcd084985996f7781ec95aaa0da2bac02f5ac21a93f6049fc085b349556bfef47696f5c5234c23e9 WHIRLPOOL 38e98e6e826b34c033efd3242d23f720327d1c5cd4ff40acf7b043c3a8acbfd7cff55189607a55cbb5a98a6c60ad298eb5ed389779d163e4ae6da3a75424e806
diff --git a/sci-libs/trilinos/trilinos-11.10.2.ebuild b/sci-libs/trilinos/trilinos-11.10.2.ebuild
deleted file mode 100644
index ac3a99ebe..000000000
--- a/sci-libs/trilinos/trilinos-11.10.2.ebuild
+++ /dev/null
@@ -1,202 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils toolchain-funcs multilib toolchain-funcs
-
-DESCRIPTION="Scientific library collection for large scale problems"
-HOMEPAGE="http://trilinos.sandia.gov/"
-SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz"
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="BSD LGPL-2.1"
-SLOT="0"
-
-IUSE="
- adolc arprec boost clp cppunit cuda eigen glpk gtest
- hdf5 hwloc hypre metis mkl mumps netcdf petsc qd qt4
- scalapack scotch sparse superlu taucs tbb test threads
- tvmet yaml zlib
-"
-
-# TODO: fix export cmake function for tests
-RESTRICT="test"
-
-RDEPEND="
- virtual/blas
- virtual/lapack
- virtual/mpi
- adolc? ( sci-libs/adolc )
- arprec? ( sci-libs/arprec )
- boost? ( dev-libs/boost )
- clp? ( sci-libs/coinor-clp )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 )
- eigen? ( dev-cpp/eigen:3 )
- gtest? ( dev-cpp/gtest )
- hdf5? ( sci-libs/hdf5[mpi] )
- hypre? ( sci-libs/hypre )
- hwloc? ( sys-apps/hwloc )
- mkl? ( sci-libs/mkl )
- metis? ( || ( sci-libs/parmetis sci-libs/metis ) )
- mumps? ( sci-libs/mumps )
- netcdf? ( sci-libs/netcdf )
- petsc? ( sci-mathematics/petsc )
- qd? ( sci-libs/qd )
- qt4? ( dev-qt/qtgui:4 )
- scalapack? ( virtual/scalapack )
- scotch? ( sci-libs/scotch )
- sparse? ( sci-libs/cxsparse sci-libs/umfpack )
- superlu? ( sci-libs/superlu )
- taucs? ( sci-libs/taucs )
- tbb? ( dev-cpp/tbb )
- tvmet? ( dev-libs/tvmet )
- yaml? ( dev-cpp/yaml-cpp )
- zlib? ( sys-libs/zlib )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${P}-Source"
-
-trilinos_conf() {
- local dirs libs d
- for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do
- dirs="${dirs};${d:2}"
- done
- [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" )
- for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do
- libs="${libs};${d:2}"
- done
- [[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" )
- dirs=""
- for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do
- dirs="${dirs};${d:2}"
- done
- [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" )
-}
-
-trilinos_enable() {
- cmake-utils_use $1 TPL_ENABLE_${2:-${1^^}}
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PN}-11.4.2-fix-install-paths.patch
-}
-
-src_configure() {
-
- local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
- -DCMAKE_INSTALL_PREFIX="${EPREFIX}"
- -DTrilinos_ENABLE_ALL_PACKAGES=ON
- -DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos"
- -DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos"
- -DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake"
- -DTPL_ENABLE_BinUtils=ON
- -DTPL_ENABLE_MPI=ON
- -DTPL_ENABLE_BLAS=ON
- -DTPL_ENABLE_LAPACK=ON
- $(cmake-utils_use test Trilinos_ENABLE_TESTS)
- $(trilinos_enable adolc)
- $(trilinos_enable arprec)
- $(trilinos_enable boost Boost)
- $(trilinos_enable boost BoostLib)
- $(trilinos_enable cppunit Cppunit)
- $(trilinos_enable clp Clp)
- $(trilinos_enable cuda)
- $(trilinos_enable cuda CUSPARSE)
- $(trilinos_enable cuda Thrust)
- $(trilinos_enable eigen Eigen)
- $(trilinos_enable gtest gtest)
- $(trilinos_enable glpk)
- $(trilinos_enable hdf5)
- $(trilinos_enable hwloc)
- $(trilinos_enable hypre)
- $(trilinos_enable metis)
- $(trilinos_enable mkl)
- $(trilinos_enable mkl PARDISO_MKL)
- $(trilinos_enable mumps)
- $(trilinos_enable netcdf Netcdf)
- $(trilinos_enable petsc)
- $(trilinos_enable qd)
- $(trilinos_enable qt4 QT)
- $(trilinos_enable scalapack)
- $(trilinos_enable scalapack BLACS)
- $(trilinos_enable scotch Scotch)
- $(trilinos_enable sparse AMD)
- $(trilinos_enable sparse CSparse)
- $(trilinos_enable sparse UMFPACK)
- $(trilinos_enable superlu SuperLU)
- $(trilinos_enable taucs)
- $(trilinos_enable tbb)
- $(trilinos_enable threads Pthread)
- $(trilinos_enable tvmet)
- $(trilinos_enable yaml yaml-cpp)
- $(trilinos_enable zlib Zlib)
- )
-
- use eigen && \
- mycmakeargs+=(
- -DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3"
- )
- use hypre && \
- mycmakeargs+=(
- -DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre"
- )
- use scotch && \
- mycmakeargs+=(
- -DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch"
- )
-
- # cxsparse is a rewrite of csparse + extras
- use sparse && \
- mycmakeargs+=(
- -DCSparse_LIBRARY_NAMES="cxsparse"
- )
-
- # mandatory blas and lapack
- trilinos_conf blas BLAS
- trilinos_conf lapack LAPACK
- use superlu && trilinos_conf superlu SuperLU
- use metis && trilinos_conf metis METIS
-
- # blacs library is included in scalapack these days
- if use scalapack; then
- trilinos_conf scalapack SCALAPACK
- mycmakeargs+=(
- -DBLACS_LIBRARY_NAMES="scalapack"
- -DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs"
- )
- fi
-
- # TODO: do we need that line?
- export CC=mpicc CXX=mpicxx && tc-export CC CXX
-
- # cmake-utils eclass patches the base directory CMakeLists.txt
- # which does not work for complex Trilinos CMake modules
- CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure
-
- # TODO:
- # python bindings with python-r1
- # fix hypre bindings
- # fix hdf5
- # cuda/thrust is untested
- # do we always need mpi? and for all packages: blah[mpi] ?
- # install docs, examples
- # see what packages are related, do we need REQUIRED_USE
- # proper use flags description
- # add more use flags/packages ?
-}
-
-src_install() {
- cmake-utils_src_install
-
- # register $(get_libdir)/trilinos in LDPATH so that the dynamic linker
- # has a chance to pick up the libraries...
- cat >> "${T}"/99trilinos <<- EOF
- LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos"
- EOF
- doenvd "${T}"/99trilinos
-}
diff --git a/sci-libs/trilinos/trilinos-11.12.1-r1.ebuild b/sci-libs/trilinos/trilinos-11.12.1-r1.ebuild
deleted file mode 100644
index 9d55c343c..000000000
--- a/sci-libs/trilinos/trilinos-11.12.1-r1.ebuild
+++ /dev/null
@@ -1,202 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils toolchain-funcs multilib toolchain-funcs
-
-DESCRIPTION="Scientific library collection for large scale problems"
-HOMEPAGE="http://trilinos.sandia.gov/"
-SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz"
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="BSD LGPL-2.1"
-SLOT="0"
-
-IUSE="
- adolc arprec boost clp cppunit cuda eigen glpk gtest
- hdf5 hwloc hypre metis mkl mumps netcdf petsc qd qt4
- scalapack scotch sparse superlu taucs tbb test threads
- tvmet yaml zlib
-"
-
-# TODO: fix export cmake function for tests
-RESTRICT="test"
-
-RDEPEND="
- virtual/blas
- virtual/lapack
- virtual/mpi
- adolc? ( sci-libs/adolc )
- arprec? ( sci-libs/arprec )
- boost? ( dev-libs/boost )
- clp? ( sci-libs/coinor-clp )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 )
- eigen? ( dev-cpp/eigen:3 )
- gtest? ( dev-cpp/gtest )
- hdf5? ( sci-libs/hdf5[mpi] )
- hypre? ( sci-libs/hypre )
- hwloc? ( sys-apps/hwloc )
- mkl? ( sci-libs/mkl )
- metis? ( || ( sci-libs/parmetis sci-libs/metis ) )
- mumps? ( sci-libs/mumps )
- netcdf? ( sci-libs/netcdf )
- petsc? ( sci-mathematics/petsc )
- qd? ( sci-libs/qd )
- qt4? ( dev-qt/qtgui:4 )
- scalapack? ( virtual/scalapack )
- scotch? ( sci-libs/scotch )
- sparse? ( sci-libs/cxsparse sci-libs/umfpack )
- superlu? ( sci-libs/superlu )
- taucs? ( sci-libs/taucs )
- tbb? ( dev-cpp/tbb )
- tvmet? ( dev-libs/tvmet )
- yaml? ( dev-cpp/yaml-cpp )
- zlib? ( sys-libs/zlib )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${P}-Source"
-
-trilinos_conf() {
- local dirs libs d
- for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do
- dirs="${dirs};${d:2}"
- done
- [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" )
- for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do
- libs="${libs};${d:2}"
- done
- [[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" )
- dirs=""
- for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do
- dirs="${dirs};${d:2}"
- done
- [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" )
-}
-
-trilinos_enable() {
- cmake-utils_use $1 TPL_ENABLE_${2:-${1^^}}
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-fix-install-paths.patch
-}
-
-src_configure() {
-
- local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
- -DCMAKE_INSTALL_PREFIX="${EPREFIX}"
- -DTrilinos_ENABLE_ALL_PACKAGES=ON
- -DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos"
- -DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos"
- -DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake"
- -DTPL_ENABLE_BinUtils=ON
- -DTPL_ENABLE_MPI=ON
- -DTPL_ENABLE_BLAS=ON
- -DTPL_ENABLE_LAPACK=ON
- $(cmake-utils_use test Trilinos_ENABLE_TESTS)
- $(trilinos_enable adolc)
- $(trilinos_enable arprec)
- $(trilinos_enable boost Boost)
- $(trilinos_enable boost BoostLib)
- $(trilinos_enable cppunit Cppunit)
- $(trilinos_enable clp Clp)
- $(trilinos_enable cuda)
- $(trilinos_enable cuda CUSPARSE)
- $(trilinos_enable cuda Thrust)
- $(trilinos_enable eigen Eigen)
- $(trilinos_enable gtest gtest)
- $(trilinos_enable glpk)
- $(trilinos_enable hdf5)
- $(trilinos_enable hwloc)
- $(trilinos_enable hypre)
- $(trilinos_enable metis)
- $(trilinos_enable mkl)
- $(trilinos_enable mkl PARDISO_MKL)
- $(trilinos_enable mumps)
- $(trilinos_enable netcdf Netcdf)
- $(trilinos_enable petsc)
- $(trilinos_enable qd)
- $(trilinos_enable qt4 QT)
- $(trilinos_enable scalapack)
- $(trilinos_enable scalapack BLACS)
- $(trilinos_enable scotch Scotch)
- $(trilinos_enable sparse AMD)
- $(trilinos_enable sparse CSparse)
- $(trilinos_enable sparse UMFPACK)
- $(trilinos_enable superlu SuperLU)
- $(trilinos_enable taucs)
- $(trilinos_enable tbb)
- $(trilinos_enable threads Pthread)
- $(trilinos_enable tvmet)
- $(trilinos_enable yaml yaml-cpp)
- $(trilinos_enable zlib Zlib)
- )
-
- use eigen && \
- mycmakeargs+=(
- -DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3"
- )
- use hypre && \
- mycmakeargs+=(
- -DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre"
- )
- use scotch && \
- mycmakeargs+=(
- -DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch"
- )
-
- # cxsparse is a rewrite of csparse + extras
- use sparse && \
- mycmakeargs+=(
- -DCSparse_LIBRARY_NAMES="cxsparse"
- )
-
- # mandatory blas and lapack
- trilinos_conf blas BLAS
- trilinos_conf lapack LAPACK
- use superlu && trilinos_conf superlu SuperLU
- use metis && trilinos_conf metis METIS
-
- # blacs library is included in scalapack these days
- if use scalapack; then
- trilinos_conf scalapack SCALAPACK
- mycmakeargs+=(
- -DBLACS_LIBRARY_NAMES="scalapack"
- -DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs"
- )
- fi
-
- # TODO: do we need that line?
- export CC=mpicc CXX=mpicxx && tc-export CC CXX
-
- # cmake-utils eclass patches the base directory CMakeLists.txt
- # which does not work for complex Trilinos CMake modules
- CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure
-
- # TODO:
- # python bindings with python-r1
- # fix hypre bindings
- # fix hdf5
- # cuda/thrust is untested
- # do we always need mpi? and for all packages: blah[mpi] ?
- # install docs, examples
- # see what packages are related, do we need REQUIRED_USE
- # proper use flags description
- # add more use flags/packages ?
-}
-
-src_install() {
- cmake-utils_src_install
-
- # register $(get_libdir)/trilinos in LDPATH so that the dynamic linker
- # has a chance to pick up the libraries...
- cat >> "${T}"/99trilinos <<- EOF
- LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos"
- EOF
- doenvd "${T}"/99trilinos
-}
diff --git a/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild b/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild
index 48adf2076..2f320296c 100644
--- a/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild
+++ b/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -25,6 +25,7 @@ IUSE="
RESTRICT="test"
RDEPEND="
+ sys-libs/binutils-libs
virtual/blas
virtual/lapack
virtual/mpi
diff --git a/sci-libs/trilinos/trilinos-12.0.1.ebuild b/sci-libs/trilinos/trilinos-12.0.1.ebuild
index 227860309..a511a3ded 100644
--- a/sci-libs/trilinos/trilinos-12.0.1.ebuild
+++ b/sci-libs/trilinos/trilinos-12.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -25,6 +25,7 @@ IUSE="
RESTRICT="test"
RDEPEND="
+ sys-libs/binutils-libs
virtual/blas
virtual/lapack
virtual/mpi
diff --git a/sci-libs/trilinos/trilinos-12.2.1.ebuild b/sci-libs/trilinos/trilinos-12.2.1.ebuild
index 5862e7390..a73261d9e 100644
--- a/sci-libs/trilinos/trilinos-12.2.1.ebuild
+++ b/sci-libs/trilinos/trilinos-12.2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -25,6 +25,7 @@ IUSE="
RESTRICT="test"
RDEPEND="
+ sys-libs/binutils-libs
virtual/blas
virtual/lapack
virtual/mpi
diff --git a/sci-libs/trilinos/trilinos-12.6.2.ebuild b/sci-libs/trilinos/trilinos-12.6.3.ebuild
index dca587c7d..707a6f1b5 100644
--- a/sci-libs/trilinos/trilinos-12.6.2.ebuild
+++ b/sci-libs/trilinos/trilinos-12.6.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -25,6 +25,7 @@ IUSE="
RESTRICT="test"
RDEPEND="
+ sys-libs/binutils-libs
virtual/blas
virtual/lapack
virtual/mpi
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 29c169c54..9abc71abf 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,5 +1,4 @@
DIST petsc-3.4.2.tar.gz 18658689 SHA256 f13b0dc978fe0dcc1df032f8142a2fd345217f02b9967936d9aac26ce4b2b52e SHA512 f839e4cfadbee720e53993eb8de74a2d82bfe2a46a418f528b4cdb2e9245b8ecafbc02d6d1718034cfe80d291095187b0946ebe237c8f985e4213c4c35bc345b WHIRLPOOL a00f4340e5dc151c57d9f5e2b764a609a508490756d8337d52bec4712fb26b8c06edf46293ed838f08ff34e1c068549ea9680657b7282cb884df4c1314c58cdb
-DIST petsc-3.5.3.tar.gz 20729341 SHA256 68e6a42f5ec75bad87f74d4df8f55ad63f0c4d996f162da6713cb3d6f566830d SHA512 7455e9a67e5bbefce8f51eeb85418cdca2b14c50c85c8f9e91c0c53744a30954915a5a3aa141969d123daf54513610502cc52051a36a2a2da82410110f7421f8 WHIRLPOOL f473eb4a4136fb74114a51e3fa4a7ff60600c77b029a600360eca0418f6412ea653a6a8d6c72f750711d9d961982aad4b4e55332661dc2c203bb8c9344e0cca4
-DIST petsc-3.6.0.tar.gz 21447278 SHA256 c27cce12d212190726d3f17b4dcc48e8afca942271f1ad32aa48b0effeaffdbe SHA512 dc0f44debc2362a47b6658a01b77f6d0f3950d0b3eb22f73bcd3f2608b1d51e169447c9e994dd4f8ebef113b8ce7f2869533645cded6098a6c66f7244f2f62da WHIRLPOOL 3004e38988eb89371212a6bd2c8fdab00246256d3ca44cee2dba952565b4e023cb73b56d38c2a897191762b4b73053ab32d8be4905b93ff70fc97356ff8cdbcf
-DIST petsc-3.6.3.tar.gz 21802974 SHA256 776e2644e4003653c56a44a6f7c02c41427af26f7c5cd9bec3aa84ed90223245 SHA512 eebfdaa4d15717fbd1a084b6019559f0567c58d72e4d4900b1e28f535e998335d8fded8c58439751ee7f95e2cb231db80cb59ba103a78e47845d6964ee7fb4fe WHIRLPOOL 90e2c6a98423bee0ca4a2bee7bd03a094e42e2de8aebc467a52fcafbed990458c6e3b3556ea073b597b88739171da16df36fa44962c0d8ec54304679d1cc5615
+DIST petsc-3.5.4.tar.gz 20750322 SHA256 a85febf92c9ed2dd9a8f4305f31cd51f9514c01d3c31fb9fb69fb6f22bd3a960 SHA512 248b0c7d6c0076f65d66a325265baa20b8846d4f6902044c4fcd16ecfc586618075c4b0f470d2a674eaa954b8b7e08afadcea783bb84ae276091728607323204 WHIRLPOOL 42e3cb00778cebb7de08b7410ff5ea3fa48964679413959f56aff10b46d436cb9d9e2317d7314bd4501fdd4fb9f964f4e572f07b58a197f3d435b6f625d91c41
DIST petsc-3.6.4.tar.gz 21792990 SHA256 eb09925a139b52b4dd5a071b3da4fe2165f1d6e8f71d410479603c9976c940f0 SHA512 3e0a69b35424c519c9af43e2323b14f5ba650bf8fc653985769fe65d618223418ebd03c166bca0b7d3affaffa51b907a50b5d9cf714f2f94d044e9c592a84965 WHIRLPOOL b94faf0140e948cb01962fd9e240e5470858e76e7d26f007056001750cc6579724fcc01cab88bfa6cbb66ced8b177ec7d7fecd171c047df0b7c03454b2ecb250
+DIST petsc-3.7.2.tar.gz 23111802 SHA256 36681dd0df97e0d5cd182d902e89f527eb8f441f05271159dac5340acb4cf0ec SHA512 f598b7312c3e9321c30f0665a3692991e977c3fc1659656cfa3329c31be0c18393e21db1d9d6f674bcb9045dad8bbfbc744ea996bd858e91f63a58aeaad556e8 WHIRLPOOL aa328f3715ead98fd546e072c51fc93c2ff2ce8698da7128abdcdf46f07706752012e21f8516f94db589d7c6d78036de38b6b54e04bddcff62360d39fd0815a4
diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
new file mode 100644
index 000000000..8d0d99330
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
@@ -0,0 +1,18 @@
+diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
+index 219a35b..ad2ed8c 100644
+--- a/config/BuildSystem/config/setCompilers.py
++++ b/config/BuildSystem/config/setCompilers.py
+@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure):
+ for language in languages:
+ flag = '-L'
+ self.pushLanguage(language)
+- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
+- if not Configure.isDarwin(self.log):
+- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
+- else:
+- testFlags = ['-Wl,-rpath,']
+- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not.
++ testFlags = []
+ if self.isSun(self.framework.getCompiler(), self.log):
+ testFlags.insert(0,'-R')
+ for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch
new file mode 100644
index 000000000..191ca18c4
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch
@@ -0,0 +1,17 @@
+diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
+index 0e2567c..bf782b5 100644
+--- a/config/PETSc/options/installDir.py
++++ b/config/PETSc/options/installDir.py
+@@ -38,12 +38,6 @@ class Configure(config.base.Configure):
+ self.installSudoMessage = ''
+ if self.framework.argDB['prefix']:
+ self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
+- try:
+- os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
+- os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
+- except:
+- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
+- self.installSudo = 'sudo '
+ else:
+ self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch))
+ self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch))
diff --git a/sci-mathematics/petsc/petsc-3.5.3.ebuild b/sci-mathematics/petsc/petsc-3.5.4.ebuild
index 7c1d0b361..7838e5d8c 100644
--- a/sci-mathematics/petsc/petsc-3.5.3.ebuild
+++ b/sci-mathematics/petsc/petsc-3.5.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -69,7 +69,7 @@ MAKEOPTS="${MAKEOPTS} -j1"
S="${WORKDIR}/${MY_P}"
src_prepare() {
- epatch "${FILESDIR}"/${P%_*}-disable-rpath.patch
+ epatch "${FILESDIR}"/${PN}-3.5.3-disable-rpath.patch
sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
}
diff --git a/sci-mathematics/petsc/petsc-3.6.3.ebuild b/sci-mathematics/petsc/petsc-3.6.3.ebuild
deleted file mode 100644
index 87537cb4f..000000000
--- a/sci-mathematics/petsc/petsc-3.6.3.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="petsc"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
- fortran hdf5 hypre mpi mumps scotch sparse superlu threads X"
-# Failed: imagemagick metis
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
- afterimage? ( X )
- hdf5? ( mpi )
- hypre? ( cxx mpi )
- mumps? ( mpi scotch )
- scotch? ( mpi )
- ^^ ( hypre superlu )
-"
-# imagemagick? ( X )
-
-RDEPEND="
- virtual/blas
- virtual/lapack
- afterimage? ( media-libs/libafterimage )
- boost? ( dev-libs/boost )
- fftw? ( sci-libs/fftw:3.0[mpi?] )
- hdf5? ( sci-libs/hdf5[mpi?] )
- hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
- mpi? ( virtual/mpi[cxx?,fortran?] )
- mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
- scotch? ( sci-libs/scotch[mpi?] )
- sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
- superlu? ( sci-libs/superlu )
- X? ( x11-libs/libX11 )
-"
-# metis? ( sci-libs/parmetis )
-# imagemagick? ( media-gfx/imagemagick )
-
-DEPEND="${RDEPEND}
- ${PYTHON_DEPS}
- virtual/pkgconfig
- dev-util/cmake
-"
-# cmake is used for parallel building
-# in some configuration setups, legacy build is used (slow)
-
-#
-# PETSc does not want its Makefiles to be invoked with anything higher than
-# -j1. The underlying build system does automatically invoke a parallel
-# build. This might not be what you want, but *hey* not your choice.
-#
-MAKEOPTS="${MAKEOPTS} -j1"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PN}-3.6.0-disable-rpath.patch \
- "${FILESDIR}"/${PN}-3.6.0-fix_sandbox_violation.patch
-
- sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
- # bug 548498
- # PETSc runs mpi processes during configure that result in a sandbox
- # violation by trying to open /proc/mtrr rw. This is not easy to
- # mitigate because it happens in libpciaccess.so called by libhwloc.so,
- # which is used by libmpi.so.
- addpredict /proc/mtrr
-
- # petsc uses --with-blah=1 and --with-blah=0 to en/disable options
- petsc_enable() {
- use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
- }
- # add external library:
- # petsc_with use_flag libname libdir
- # petsc_with use_flag libname include linking_libs
- petsc_with() {
- local myuse p=${2:-${1}}
- if use ${1}; then
- myuse="--with-${p}=1"
- if [[ $# -ge 4 ]]; then
- myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
- shift 3
- myuse="${myuse} --with-${p}-lib=$@"
- else
- myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
- fi
- else
- myuse="--with-${p}=0"
- fi
- echo ${myuse}
- }
-
- # select between configure options depending on use flag
- petsc_select() {
- use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
- }
-
- local mylang
- local myopt
-
- use cxx && mylang="cxx" || mylang="c"
- use debug && myopt="debug" || myopt="opt"
-
- # environmental variables expected by petsc during build
- export PETSC_DIR="${S}"
- export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
- if use debug; then
- strip-flags
- filter-flags -O*
- fi
-
- # C Support on Cxx builds is enabled if possible
- # i.e. when not using complex scalars
- # (no complex type for both available at the same time)
-
- # run petsc configure script
- econf \
- scrollOutput=1 \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}" \
- LDFLAGS="${LDFLAGS}" \
- --with-shared-libraries \
- --with-single-library \
- --with-clanguage=${mylang} \
- $(use cxx && ! use complex-scalars && echo "with-c-support=1") \
- --with-petsc-arch=${PETSC_ARCH} \
- --with-precision=double \
- --with-gnu-compilers \
- --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
- $(petsc_enable debug debugging) \
- $(petsc_enable mpi) \
- $(petsc_select mpi cc mpicc $(tc-getCC)) \
- $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
- $(petsc_enable fortran) \
- $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
- $(petsc_enable mpi mpi-compilers) \
- $(petsc_select complex-scalars scalar-type complex real) \
- --with-windows-graphics=0 \
- --with-matlab=0 \
- --with-cmake=cmake \
- $(petsc_enable threads pthread) \
- $(petsc_with afterimage afterimage \
- /usr/include/libAfterImage -lAfterImage) \
- $(petsc_with hdf5) \
- $(petsc_with hypre hypre \
- /usr/include/hypre -lHYPRE) \
- $(petsc_with sparse suitesparse) \
- $(petsc_with superlu superlu \
- /usr/include/superlu -lsuperlu) \
- $(petsc_with X x) \
- $(petsc_with X x11) \
- $(petsc_with scotch ptscotch \
- /usr/include/scotch \
- [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
- $(petsc_with mumps scalapack \
- /usr/include/scalapack -lscalapack) \
- $(petsc_with mumps mumps \
- /usr/include \
- [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
- --with-imagemagick=0 \
- --with-python=0 \
- $(petsc_with boost) \
- $(petsc_with fftw)
-
-# not yet tested:
-# python bindings, netcdf, fftw
-
-# failed dependencies, perhaps fixed in upstream soon:
-# $(petsc_with metis parmetis) \ # needs metis too (>=5.0.2)
-# $(petsc_with imagemagick imagemagick \
-# /usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \
-# $(petsc_enable threads pthreadclasses) \
-}
-
-src_install() {
- # petsc install structure is very different from
- # installing headers to /usr/include/petsc and lib to /usr/lib
- # it also installs many unneeded executables and scripts
- # so manual install is easier than cleanup after "emake install"
- insinto /usr/include/${PN}
- doins include/*.h*
- insinto /usr/include/${PN}/${PETSC_ARCH}/include
- doins ${PETSC_ARCH}/include/*
- if use fortran; then
- insinto /usr/include/${PN}/finclude
- doins -r include/${PN}/finclude/*
- fi
- if ! use mpi ; then
- insinto /usr/include/${PN}/mpiuni
- doins include/mpiuni/*.h
- fi
- insinto /usr/include/${PN}/conf
- doins lib/${PN}/conf/{variables,rules,test}
- insinto /usr/include/${PN}/${PETSC_ARCH}/conf
- doins ${PETSC_ARCH}/lib/${PN}/conf/{petscrules,petscvariables,RDict.db}
- insinto /usr/include/${PN}/private
- doins include/${PN}/private/*.h
-
- # fix configuration files: replace "${S}" by installed location
- sed -i \
- -e "s:"${S}"::g" \
- "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \
- "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
- sed -i \
- -e "s:-I/include:-I${EPREFIX}/usr/include/${PN}:g" \
- -e "s:-I/linux-gnu-cxx-opt/include:-I${EPREFIX}/usr/include/${PN}/${PETSC_ARCH}/include/:g" \
- "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
- sed -i \
- -e "s:usr/lib:usr/$(get_libdir):g" \
- "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die
-
- # add information about installation directory and
- # PETSC_ARCH to environmental variables
- cat >> 99petsc <<- EOF
- PETSC_ARCH=${PETSC_ARCH}
- PETSC_DIR=${EPREFIX}/usr/include/${PN}
- EOF
- doenvd 99petsc
-
- dolib.so ${PETSC_ARCH}/lib/*.so
- dolib.so ${PETSC_ARCH}/lib/*.so.*
-
- if use doc ; then
- einfo "installing documentation (this could take a while)"
- dodoc docs/manual.pdf
- dohtml -r docs/*.html docs/changes docs/manualpages
- fi
-}
diff --git a/sci-mathematics/petsc/petsc-3.6.0.ebuild b/sci-mathematics/petsc/petsc-3.7.2.ebuild
index 58ff3bd9c..3ca12fff9 100644
--- a/sci-mathematics/petsc/petsc-3.6.0.ebuild
+++ b/sci-mathematics/petsc/petsc-3.7.2.ebuild
@@ -64,14 +64,16 @@ DEPEND="${RDEPEND}
# -j1. The underlying build system does automatically invoke a parallel
# build. This might not be what you want, but *hey* not your choice.
#
-MAKEOPTS="${MAKEOPTS} -j1"
+# V=1 enables verbose output with full compiler and linker invocation
+#
+MAKEOPTS="${MAKEOPTS} -j1 V=1"
S="${WORKDIR}/${MY_P}"
src_prepare() {
epatch \
- "${FILESDIR}"/${P%_*}-disable-rpath.patch \
- "${FILESDIR}"/${P%_*}-fix_sandbox_violation.patch
+ "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
+ "${FILESDIR}"/${PN}-3.7.0-fix_sandbox_violation.patch
sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
}
@@ -135,8 +137,9 @@ src_configure() {
# run petsc configure script
econf \
scrollOutput=1 \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}" \
+ FFLAGS="${FFLAGS} -fPIC" \
+ CFLAGS="${CFLAGS} -fPIC" \
+ CXXFLAGS="${CXXFLAGS} -fPIC" \
LDFLAGS="${LDFLAGS}" \
--with-shared-libraries \
--with-single-library \
@@ -228,6 +231,11 @@ src_install() {
-e "s:usr/lib:usr/$(get_libdir):g" \
"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die
+ # fix the include path of petscvariables in lib/${PN}/conf/variables
+ # bug #559172
+ sed -i -e 's#lib/petsc/conf/#conf/#g' \
+ "${ED}"/usr/include/${PN}/conf/variables || die
+
# add information about installation directory and
# PETSC_ARCH to environmental variables
cat >> 99petsc <<- EOF